Figure 1

Unsupervised approach to identify breast cancer subtypes. (A) Correlation of breast tumor samples with the previously identified five subtypes of breast tumors. 526 out of 552 previously identified "intrinsic" genes were cross-mapped to Applied Biosystems Human Genome Survey Microarray and used for centroid correlation analysis and hierarchical clustering. Correlations with the centroids of the five subtypes were calculated for each sample from this study (the two microarray replicates for each sample were averaged). Samples were assigned to a subtype with which it showed the highest correlation using a cutoff value of 0.2. (B) Unsupervised hierarchical clustering of 20 breast tumor tissues analyzed by AB arrays using the 526 mapped intrinsic genes (the two microarray replicates for each sample are shown). The level of expression of each gene in each sample, relative to the median level of expression of that gene across all the samples, is represented using a red-black-green color scale as shown in the key (green: below median; black: equal to median; red: above median). (Left panel): Scaled down representation of the entire cluster of the 526 intrinsic genes and 20 tissue samples. (Right panel): Experimental dendrogram displaying the clustering of the tumors into three distinct subgroups. Branches are color-coded according to the subtype with which the corresponding tumor sample showed the highest correlation. Tumors with low correlation (< 0.2) with a specific subtype are indicated by gray branches.